--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_GFF_Features.py	Mon May 09 08:26:30 2022 +0000
@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+# Guruprasad Ananda
+"""
+Extract features from GFF file.
+
+usage: %prog input1 out_file1 column features
+"""
+from __future__ import print_function
+
+import sys
+
+from bx.cookbook import doc_optparse
+
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+
+def main():
+    # Parsing Command Line here
+    options, args = doc_optparse.parse(__doc__)
+
+    try:
+        inp_file, out_file, column, features = args
+    except ValueError:
+        stop_err("One or more arguments is missing or invalid.\nUsage: prog input output column features")
+    try:
+        column = int(column)
+    except ValueError:
+        stop_err("Column %s is an invalid column." % column)
+
+    if features is None:
+        stop_err("Column %d has no features to display, select another column." % (column + 1))
+
+    fo = open(out_file, "w")
+    for line in open(inp_file):
+        line = line.rstrip("\r\n")
+        if line and line.startswith("#"):
+            # Keep valid comment lines in the output
+            fo.write("%s\n" % line)
+        else:
+            try:
+                if line.split("\t")[column] in features.split(","):
+                    fo.write("%s\n" % line)
+            except Exception:
+                pass
+    fo.close()
+
+    print("Column %d features: %s" % (column + 1, features))
+
+
+if __name__ == "__main__":
+    main()